When I install an application template, say, Blender-Pro, via the provided commands in Blender 2.79, it is copied to the correct location stated in the manual:

But the UI does not list it:

But here comes the best part: If I move the entire folder bl_app_templates_user from the correct location to my local drive, that is C:\Users\MYUSER\AppData\Roaming\Blender Foundation\Blender\2.79\scripts\startup, it IS recognized:

So it seems as if the Application System is entirely ignoring the BLENDER_USER_SCRIPTS variable.

It's just not using BLENDER_SYSTEM_SCRIPTS and BLENDER_USER_SCRIPTS variables for this.

Ideally it would use we could just use script_paths() in app_template_paths() , but it's a bit more complicated because the subdirectory is different depending if it's a system or user directory. (I'm not sure what the reasoning for that was).